The federal government is seeking billions of dollars in penalties and damages from the company that did the background security check on NSA leaker Edward Snowden.

The Justice Department says in a new court filing that U.S. Investigations Services Inc., the largest of the several firms that the government contracts with to investigate current and prospective federal employees, lied about 665,000 checks it conducted between 2008 and 2012.

USIS devised an elaborate scheme in which it told the government it had completed probes of people whose backgrounds it had not, in fact, thoroughly vetted, according to a 25-page document filed Wednesday in an Alabama court as part of an ongoing civil lawsuit against the Falls Church, Va.-based firm.

While the government brief doesn't say that USIS submitted a phony security check on Snowden, that check was purportedly completed in 2011 during the four-year period described by the Justice Department.

The 665,000 allegedly phony checks represented 40 percent of all checks conducted by USIS for the federal government, which means the chances are two in five that Snowden was not thoroughly vetted while working as a computer-security contractor for the National Security Agency.

The government also hired USIS to do the background check on Aaron Alexis, another contract employee who shot and killed 12 people Sept. 16 last year at the Washington Navy Yard.

Ellen Davis, a USIS spokeswoman said in a statement that the alleged fraudulent behavior was limited to "a small group of individuals" and runs contrary to the company's "values and commitment to exceptional service."